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- PDB-3o8i: Structure of 14-3-3 isoform sigma in complex with a C-Raf1 peptid... -

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Basic information

Entry
Database: PDB / ID: 3o8i
TitleStructure of 14-3-3 isoform sigma in complex with a C-Raf1 peptide and a stabilizing small molecule fragment
Components
  • 14-3-3 binding site peptide of RAF proto-oncogene serine/threonine-protein kinase
  • 14-3-3 protein sigma
KeywordsPEPTIDE BINDING PROTEIN / Protein-Protein Complex / 14-3-3 / Protein-protein interaction / Phosphorylation
Function / homology
Function and homology information


death-inducing signaling complex assembly / intermediate filament cytoskeleton organization / type B pancreatic cell proliferation / regulation of Rho protein signal transduction / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / Rap1 signalling / insulin secretion involved in cellular response to glucose stimulus / Negative feedback regulation of MAPK pathway / IFNG signaling activates MAPKs ...death-inducing signaling complex assembly / intermediate filament cytoskeleton organization / type B pancreatic cell proliferation / regulation of Rho protein signal transduction / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / Rap1 signalling / insulin secretion involved in cellular response to glucose stimulus / Negative feedback regulation of MAPK pathway / IFNG signaling activates MAPKs / GP1b-IX-V activation signalling / regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / ERBB2-ERBB3 signaling pathway / keratinization / regulation of cell-cell adhesion / face development / pseudopodium / neurotrophin TRK receptor signaling pathway / regulation of cell differentiation / thyroid gland development / cAMP/PKA signal transduction / Regulation of localization of FOXO transcription factors / somatic stem cell population maintenance / keratinocyte proliferation / extrinsic apoptotic signaling pathway via death domain receptors / phosphoserine residue binding / MAP kinase kinase kinase activity / Activation of BAD and translocation to mitochondria / negative regulation of keratinocyte proliferation / type II interferon-mediated signaling pathway / establishment of skin barrier / negative regulation of protein localization to plasma membrane / negative regulation of protein-containing complex assembly / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Schwann cell development / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of stem cell proliferation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / activation of adenylate cyclase activity / positive regulation of peptidyl-serine phosphorylation / positive regulation of protein localization / response to muscle stretch / myelination / CD209 (DC-SIGN) signaling / positive regulation of cell adhesion / protein sequestering activity / insulin-like growth factor receptor signaling pathway / negative regulation of innate immune response / protein export from nucleus / release of cytochrome c from mitochondria / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / thymus development / positive regulation of protein export from nucleus / negative regulation of protein kinase activity / stem cell proliferation / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / RAF activation / wound healing / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / Stimuli-sensing channels / intrinsic apoptotic signaling pathway in response to DNA damage / Signaling by RAF1 mutants / Negative regulation of MAPK pathway / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / Signaling by BRAF and RAF1 fusions / MAPK cascade / intracellular protein localization / insulin receptor signaling pathway / regulation of protein localization / positive regulation of cell growth / regulation of apoptotic process / mitochondrial outer membrane / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity
Similarity search - Function
Raf-like Ras-binding domain / Raf-like Ras-binding / Ras-binding domain (RBD) profile. / Raf-like Ras-binding domain / Diacylglycerol/phorbol-ester binding / 14-3-3 domain / : / Delta-Endotoxin; domain 1 / Phorbol esters/diacylglycerol binding domain (C1 domain) / 14-3-3 protein sigma ...Raf-like Ras-binding domain / Raf-like Ras-binding / Ras-binding domain (RBD) profile. / Raf-like Ras-binding domain / Diacylglycerol/phorbol-ester binding / 14-3-3 domain / : / Delta-Endotoxin; domain 1 / Phorbol esters/diacylglycerol binding domain (C1 domain) / 14-3-3 protein sigma / Zinc finger phorbol-ester/DAG-type signature. / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / C1-like domain superfamily / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site / 14-3-3 proteins signature 1. / 14-3-3 protein / 14-3-3 homologues / 14-3-3 domain / 14-3-3 domain superfamily / 14-3-3 protein / Ubiquitin-like domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
6,6-dihydroxy-1-methoxyhexan-2-one / RAF proto-oncogene serine/threonine-protein kinase / 14-3-3 protein sigma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsOttmann, C. / Rose, R. / Kaiser, M. / Kuhenne, P.
CitationJournal: Mol.Cell.Biol. / Year: 2010
Title: Impaired Binding of 14-3-3 to C-RAF in Noonan Syndrome Suggests New Approaches in Diseases with Increased Ras Signaling
Authors: Molzan, M. / Schumacher, B. / Ottmann, C. / Baljuls, A. / Polzien, L. / Weyand, M. / Thiel, P. / Rose, R. / Rose, M. / Kuhenne, P. / Kaiser, M. / Rapp, U.R. / Kuhlmann, J. / Ottmann, C.
History
DepositionAug 3, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 29, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 14-3-3 protein sigma
B: 14-3-3 binding site peptide of RAF proto-oncogene serine/threonine-protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1893
Polymers28,0262
Non-polymers1621
Water2,936163
1
A: 14-3-3 protein sigma
B: 14-3-3 binding site peptide of RAF proto-oncogene serine/threonine-protein kinase
hetero molecules

A: 14-3-3 protein sigma
B: 14-3-3 binding site peptide of RAF proto-oncogene serine/threonine-protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3776
Polymers56,0534
Non-polymers3242
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area4440 Å2
ΔGint-26 kcal/mol
Surface area22420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.310, 114.860, 64.930
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein 14-3-3 protein sigma / Stratifin / Epithelial cell marker protein 1


Mass: 26818.242 Da / Num. of mol.: 1 / Fragment: C-terminal deletion
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SFN, HME1 / Plasmid: pProEX-Htb / Production host: Escherichia coli (E. coli) / References: UniProt: P31947
#2: Protein/peptide 14-3-3 binding site peptide of RAF proto-oncogene serine/threonine-protein kinase / Proto-oncogene c-RAF / cRaf / Raf-1


Mass: 1208.175 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthesized Phospho-Peptide / References: UniProt: P04049
#3: Chemical ChemComp-M1T / 6,6-dihydroxy-1-methoxyhexan-2-one


Mass: 162.184 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H14O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.77 Å3/Da / Density % sol: 55.61 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.095M HEPES Na, 26.6%(v/v) PEG400, 0.19M CaCl2, 5%(v/v) Glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99986 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 11, 2009
RadiationMonochromator: Si(111) monochromator (horizontal) and Dynamically bendable mirror (vertical)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99986 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 21324 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 33.855 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 14.37
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2-2.30.4290.3494.130160724372210.499.7
2.3-2.80.1750.1449.425914621561990.16599.7
2.8-3.50.070.06419.415807381738060.07399.7
3.5-40.0320.04131.65492134413400.04699.7
4-50.0240.03336.45321133413260.03799.4
5-100.0210.02637.44965127312690.0399.7
10-150.0160.02140.84281401300.02592.9
15-200.0220.02338.510537330.02889.2
2031

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
ProDCdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IQU

3iqu


Resolution: 2→19.58 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.925 / Occupancy max: 1 / Occupancy min: 0.3 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2388 1067 5 %RANDOM
Rwork0.1851 ---
obs0.1877 21324 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 73.42 Å2 / Biso mean: 29.5154 Å2 / Biso min: 8.35 Å2
Baniso -1Baniso -2Baniso -3
1-2.33 Å20 Å20 Å2
2---1.65 Å20 Å2
3----0.69 Å2
Refinement stepCycle: LAST / Resolution: 2→19.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1785 0 11 163 1959
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0221900
X-RAY DIFFRACTIONr_angle_refined_deg1.8011.9852570
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4615240
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.20124.54588
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.75415.042354
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7251514
X-RAY DIFFRACTIONr_chiral_restr0.1340.2288
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211423
X-RAY DIFFRACTIONr_mcbond_it1.5861.51176
X-RAY DIFFRACTIONr_mcangle_it2.59321894
X-RAY DIFFRACTIONr_scbond_it4.0583724
X-RAY DIFFRACTIONr_scangle_it6.2634.5675
X-RAY DIFFRACTIONr_rigid_bond_restr2.75631900
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 77 -
Rwork0.226 1464 -
all-1541 -
obs--100 %

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